Hind III Digest of PCR Products

Jayakumar, R R.Jayakumar at roswellpark.org
Sun Jan 29 16:13:33 EST 2006

How do you know that the end is not being digested? Is it from the
ligation results or the fragments don't self ligate after digestion and
   Check and see if digested PCR fragments form dimers or trimers (if
both ends have HindIII) upon self-ligation.

-----Original Message-----
From: methods-bounces at oat.bio.indiana.edu
[mailto:methods-bounces at oat.bio.indiana.edu] On Behalf Of Mark Blenner
Sent: Saturday, January 28, 2006 1:56 PM
To: methods at magpie.bio.indiana.edu
Subject: Hind III Digest of PCR Products

I have a 790 bp PCR fragment I am trying to ligate
into a 7400bp vector - some data suggests there may be
some difficulties in cutting the HindIII  at the end
of my PCR fragment, but I've added 6 extra basepairs
and still doesnt work. Anyone seen this before? 

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